The Hopp–Woods hydrophilicity scale of amino acid

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

s is a method of ranking the amino acids in a protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 according to their water solubility

Water solubility

Water is a bent, polar compound and possesses the ability to Hydrogen bond. As a result, it has unique solubility characteristics as a solvent and functions differently at different temperatures.-Sources:...

 in order to search for surface locations on proteins, and especially those locations that tend to form strong interactions with other macromolecule

Macromolecule

A macromolecule is a very large molecule commonly created by some form of polymerization. In biochemistry, the term is applied to the four conventional biopolymers , as well as non-polymeric molecules with large molecular mass such as macrocycles...

s such as proteins, DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

, and RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

.

Given the amino acid sequence of any protein, likely interaction sites can be identified by taking the moving average of six amino acid hydrophilicity values along the polypeptide chain, and looking for local peaks in the data plot.

In subsequent papers after their initial publication of the method, Hopp and Woods demonstrated that the data plots, or hydrophilicity profiles, contained much information about protein folding

Protein folding

Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....

, and that the hydrophobic valleys of the profiles corresponded to internal structures of proteins such as beta-strands and alpha-helices

Alpha helix

A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...

. Furthermore, long hydrophobic valleys were shown to correspond quite closely to the membrane-spanning helices identified by the later-published Kyte and Doolittle hydropathic plotting method.